Discussions

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  runDLKcat(): use DLKcat.tsv in a different directory

  PkiwiBird asked Aug 8, 2024 in Q&A · Closed · Unanswered

  

  

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  No EC number in ec.eccodes although EC is in uniprot.tsv

  PkiwiBird asked Aug 14, 2024 in Q&A · Unanswered

  

  

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  Improvement for Protein Usage Calculation in reportEnzymeUsage

  HossFir started Jul 29, 2024 in Ideas

  

  

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  GECKO Model Adapter. Is it possible to define more than one compartment with the parameter 'obj.params.enzyme_comp' ?

  Zyklotron42 asked Jul 18, 2024 in Q&A · Answered

  

  

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  Clarification on the flexibilizeEnzConcs Function and Its Impact on Enzyme Concentrations and kcat Values

  HossFir started Jul 5, 2024 in GECKO3

  

  

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  runDLKcat() cannot find path to data

  PkiwiBird asked May 19, 2024 in Q&A · Answered

  

  

  

  

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  What should uniprot.geneIDfield be for NCBI Gene identifiers

  PkiwiBird asked Mar 19, 2024 in Q&A · Closed · Unanswered

  

  

  

  

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  genes reported in noUniprot can actually be found in data/uniprot.tsv

  PkiwiBird asked May 19, 2024 in Q&A · Answered

  

  

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  ecFSEOF Output Interpretation GECKO 3.1.3

  HossFir started Apr 30, 2024 in GECKO3

  

  

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  why error using loadDatabases when internet is working

  PkiwiBird asked Mar 24, 2024 in Q&A · Answered

  

  

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  Source of data for spontaneousReactions.tsv in HumanGEMAdapter.m

  PkiwiBird asked Mar 22, 2024 in Q&A · Closed · Unanswered

  

  

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  How to deal with version of gene id in modeladapter file, obj.params.kegg.geneID ?

  PkiwiBird asked Feb 14, 2024 in Q&A · Answered

  

  

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  Help: ComplexData for Non-Model Organism

  HossFir started Jan 24, 2024 in GECKO3

  

  

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  format of customKcats.tsv with and/or relations

  help

  HossFir started Jan 23, 2024 in GECKO3

  

  

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  ecFSEOF implementation in GECKO 3.1.2

  JBiaggi started Dec 5, 2023 in GECKO3

  

  

  

  

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  Changes in ecFSEOF: GECKO 2.0 -> 3.0

  JBiaggi asked Sep 18, 2023 in Q&A · Answered

  

  

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  What is params.c_UptakeExp?

  wshao1 asked Sep 5, 2023 in Q&A · Unanswered

  

  

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  DLKcat Docker reference format error

  wshao1 asked Aug 23, 2023 in Q&A · Closed · Unanswered

  

  

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  Integration of proteomics data

  alinarekena asked Jul 27, 2023 in Q&A · Unanswered

  

  

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  ecFactory as part of GECKO

  enhancement question

  ae-tafur started Apr 5, 2023 in GECKO3

  

  

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  Preprocessing BRENDA data

  feiranl started Sep 29, 2022 in GECKO3

  

  

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  EnzymeInfo structure with complex information

  edkerk started Sep 27, 2022 in GECKO3

  

  

  

  

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  Future GECKO architecture

  edkerk started Jul 7, 2022 in GECKO3 · Closed

  

  

  

  

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